[gmx-users] Re: nve run of carbon nanotube

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 16 16:49:00 CET 2010

Vitaly Chaban wrote:
>>  Dear Gmx-users,
>>  I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
>>  parameters of carbon nanotube from "Strong correlations and Fickian
>> water water
>> diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
>> Maiti Chandan
>> Dasgupta and A. K. Sood, JCP, 126 124704 (2007)".
>> During the run my carbon nanotube does not remain cylindrical, it
>> bends inwards and forms
>> a dumbell shaped structure, also it rotates in space and does not
>> remain fixed.
>> My questions are
>> 1) are my itp and mdp parameters correct
> Formally correct.

Flexible water should not be used for MD.  All the water models in Gromacs 
should be rigid.  As such, "define = -DFLEXIBLE" is incorrect.

>> 2) how do i determine if system is really in ground state or stable
> You CNT should not migrate within a box, for sure. I believe it is
> principally impossible in spite of the force field parameters that can
> be used. You may want to upload the video with the system dynamics on
> the YOUTUBE for us to look at.
>> 3) temprature keeps on rising as the simulation proceeds is this all right?
> No. For how much does it increase?

Using a plain cutoff for the electrostatics could be causing this.


> --
> Dr. Vitaly Chaban


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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